Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.10.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.10499	0.63
27DAP/17DAP	1.38163	0.592
39DAP/27DAP	0.97227	0.7
41DAP/39DAP	0.94243	0.766
42DAP/41DAP	1.00961	1
43DAP/42DAP	1.38157	0.309
47DAP/43DAP	1.36062	0.278
52DAP/47DAP	0.81818	0.612
57DAP/52DAP	1.13648	0.886

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1214	0.35
17DAP/reference	0.92476	0.24
27DAP/reference	0.96407	0.595
39DAP/reference	0.95749	0.587
41DAP/reference	0.76418	0.016
42DAP/reference	0.95203	0.218
43DAP/reference	0.94596	0.331
47DAP/reference	1.03974	0.752
52DAP/reference	1.05695	0.73
57DAP/reference	0.98725	0.61

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.35111	0.068
27DAP/17DAP	0.76327	0.206
39DAP/27DAP	0.63787	0.035
41DAP/39DAP	0.95531	0.885
42DAP/41DAP	1.22594	0.038
43DAP/42DAP	0.89363	0.101
47DAP/43DAP	0.89289	0.286
52DAP/47DAP	0.96576	0.893
57DAP/52DAP	0.72592	0.215
57DAP/7DAP	0.78315

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00424	1
17DAP/reference	0.69818	0.011
27DAP/reference	0.66524	0.01
39DAP/reference	0.62071	0.011
41DAP/reference	0.60422	0.013
42DAP/reference	0.57796	0.01
43DAP/reference	0.43399	0.009
47DAP/reference	0.52027	0.034
52DAP/reference	0.45947	0.01
57DAP/reference	0.63988	0.01

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98988	0.786
17DAP/reference	0.993	0.766
27DAP/reference	1.08542	0.781
39DAP/reference	0.94582	0.37
41DAP/reference	0.8864	0.194
42DAP/reference	0.76176	0.039
43DAP/reference	0.82976	0.14
47DAP/reference	0.74697	0.023
52DAP/reference	0.83371	0.047
57DAP/reference	0.835	0.035

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.3888	0.017
17DAP/reference	1.29894	0.136
27DAP/reference	0.88437	0.126
39DAP/reference	0.83004	0.018
41DAP/reference	0.81982	0.107
42DAP/reference	0.78017	0.041
43DAP/reference	0.8627	0.206
47DAP/reference	0.96485	0.465
52DAP/reference	0.74389	0.144
57DAP/reference	1.08027	0.717

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.74476	1
26DAP/20DAP	1.07667	1
34DAP/26DAP	1.12567	1
51DAP/34DAP	1.18043	0.429
52DAP/51DAP	0.91477	1
53DAP/52DAP	0.88699	0.595
55DAP/53DAP	0.92386	0.725
57DAP/55DAP	0.92614	0.652
62DAP/57DAP	1.05168	0.868
68DAP/62DAP	0.85762	0.641
68DAP/14DAP	0.87476	1

Experiment: Tomato (breaker-stage) vs. Pepper (breaker-stage)

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.10357	0.814

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.93751	0.618
Mature Green Tomato/Ripe Tomato	1.4971	0.019
Immature Eggplant/Mature Eggplant	0.98158	1
Ripe Pepper/Ripe Tomato	1.75702	0.256
Mature Eggplant/Ripe Tomato	3.43254	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.6202	0.536
1-1-2/M82	0.99077
12-2/M82	1.14175
12-4/M82	0.8308
1-3/M82	0.66945
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	3.05797
3-2/M82	1.1123	0.426
4-1-1/M82	1.30658	1
4-1/M82	N/A	N/A
4-3-2/M82	1.23615
4-3/M82	1.81293	1
5-3/M82	0.73238	0.642
6-2/M82	1.51153
6-3/M82	N/A	N/A
7-1/M82	0.81482
7-2/M82	N/A	N/A
9-3-2/M82	1.98453

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.05123	0.365
IL2-6/WTpooled	0.94264	1
IL7-5/WTpooled	1.23438
IL7-3/WTpooled	1.04629	1
IL12-4/WTpooled	0.87489	0.71
IL1-4/WTpooled	0.96065	1
WT/WTpooled	0.99753	1

Experiment: Transcriptional changes determined by expression of the Xanthomonas AvrRxv effector in resistant tomato plants

hybridization	ratio	FDR (corrected p value)
10 h post inoculation	0.98906	1

Experiment: Time course of DC3000 vs delta hrp on tomato Prf-3

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91239	1
DC3000/delta hrp 6h	1.02656	1
DC3000/delta hrp 12h	1.28828	1
DC3000/delta hrp 24h	1.2011	0.212

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.76763	0.028
DC3000 delta B/DC3000 delta AB	0.75156	0.03

Experiment: Matt's wild cherry tomato vs. Phytophthora infestans

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.73468	0.328
Exp 36h	0.74986	0.539
Exp 60h	0.68585	0.32

Experiment: Gene expression profiling of infection of tomato by Phytophthora infestans in the field

hybridization	ratio	FDR (corrected p value)
self-self	0.99784	1
Var 0h	1.0274	1
Var 12h I row2-row1	0.87528	0.565
Var 12h NI row2-row1	0.9683	0.906
Var 36h I row2-row1	1.03756	1
Var 36h NI row2-row1	1.15359	1
Var 60h I row2-row1	0.91309	0.285
Var 60h NI row2-row1	1.25446	0.904
Time course 0hI-0hNI	0.96443	0.835
Time course 12hI-12hNI	0.94918	0.637
Time course 36hI-36hNI	0.83052	0.067
Time course 60hI-60hNI	0.20833	0.005

Experiment: Transcriptional profiling of the tomato fruit pericarp tissue: fruits overexpressing yeast ySAMdc gene and controls

hybridization	ratio	FDR (corrected p value)
transgenic ySAMdc/azygous control (mature green)	1.05001	0.326
transgenic ySAMdc/azygous control (breaker)	0.87867	0.134
transgenic ySAMdc/azygous control (red)	1.52114	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.73199	0.064

Experiment: Microarray Analysis on Salt Stress Affected Genes in Tomato Seedlings

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.94907	0.233

Experiment: Transcriptional Profiling of high pigment-2dg Tomato Mutant Fruit

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	4.64372	0.083
Manapal/WT (break)	2.40808	0.183
Manapal/WT (red)	2.25746	0.126